[Chimera-users] Protskin

[Elaine Meng]

On Jan 15, 2009, at 7:07 AM, Patton, John (NIH/NIAID) wrote:
>
> Hi Elaine,
> Do you have any information concerning using Protskin in conjunction  
> with
> Chimera? The only information I have come across applies to PyMol.
> Thanks,
> John

Hi John,
I haven't tried Protskin, but my understanding is that its purpose is  
to map conservation in a multiple sequence alignment to protein display.
(Protskin page: <http://www.mcgnmr.ca/ProtSkin/intro/> )

Chimera itself can
(A) read your multiple sequence alignment (many formats, just use  
File... Open)

(B) calculate any of several measures of conservation (entropy,  
variability, etc.)
     - in the sequence window menu, choose Preferences... Analysis,  
set "Conservation style" to "AL2CO" to access further options for  
calculating conservation, which is shown as a histogram above the  
alignment
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#conservation 
 >

(C) show them on your structure(s) with any color mapping you desire,  
or with "worm" thickness
     - any open structure(s) will associate automatically with  
sequence(s) in the alignment
     - in the sequence window menu, choose Structure... Render by  
Conservation, change attribute to "mavConservation" and show with  
color or worms
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render 
 >

Example image, 1bzm colored by conservation in PFAM Carb_anhydrase  
seed alignment:
<http://www.cgl.ucsf.edu/chimera/feature_highlights/1bzm-al2co-highlight.png 
 >

This tutorial includes coloring by conservation:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>

Back to ProtSkin:
-----------------
It sounds like ProtSkin emits some file listing the residues and  
associated values.  Certainly you could reformat that into a Chimera  
"define attribute" file, read it in, and then show the values as in  
(C) above.  Since Chimera already performs the preceding steps quite  
well and with many powerful options, there hasn't been much impetus to  
hooking it up to ProtSkin.  However, I don't see any barrier other  
than your needing to convert the output file into the simple "define  
attribute" format described here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile 
 >

Getting a sequence alignment:
-----------------------------
Perhaps you didn't already have a sequence alignment, and find  
ProtSkin to be helpful in generating one.  There are many alternative  
approaches.  For example, the ConSurf server does a great job of  
automatically generating an alignment of a diverse set of sequences  
related to your single uploaded structure.
(ConSurf server: <http://consurf.tau.ac.il/> )

There are more ideas in this page I wrote on "sources of sequence  
alignments" for use in Chimera:
<http://www.cgl.ucsf.edu/home/meng/sources.html>

I would be happy provide more detailed help on using Chimera to color  
by conservation as it applies to your system of interest, i.e. feel  
free to write back.  Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html